how to import a 1000 genome project vcf file (chromosome file) into a mysql database

Question

[pinikoma]

Hi All

I would like to import / upload a 1000 genome project vcf file (chromosome file) into a mysql database using sql.

If there are existing mysql dumps, please tell where I can find them.

Also if there is an official way-script I would love to see it

Thanks, pini.

[Pierre Lindenbaum]

See Do People Import Vcf Files Into Databases?, Vcf Database Table Structure. But inserting a VCF into a database is a bad idea unless you want to expose your data. Tabix/Tribble indexes should do the job.

[Emily]

Meanwhile, Ensembl has stopped putting a lot of variation data into MySQL and instead are storing everything in VCFs (much more compact).

[karl.stamm]

How would you import anything to a database? See programming forums for a batch insert command.